Hi all!
Sorry to bother with a simple question- I have read through all the cummeRbund posts and tutorials but I seem to be stuck right at the start!
I have ran RNA-seq analyses on galaxy online- tophat, cufflinks, cuffmerge, and cuffdiff. I would now like to visualize results in cummeRbund. I downloaded the cuffdiff files (11 each for two groups) off galaxy and they are in .tabular format. I installed cummeRbund, and ran the following. It does not work. Could the issue be that files should be in .db format? I don't know where the cuffData.db file came from- it appeared before I had even downloaded the cuffdiff files.
> source("http://bioconductor.org/biocLite.R")
> biocLite("cummeRbund")
> getwd()
> setwd("C:/Users/caetano1/Downloads/SEDENTARYDFF")
> list.files()
> library(cummeRbund)
> cuff= readCufflinks (dbFile = "cuffData.db",
+ geneFPKM = "CuffdiffSEDENTARY__gene_FPKM_tracking.tabular",
+ geneDiff = "CuffdiffSEDENTARY__CDS_FPKM_differential_expression_testing.tabular",
+ isoformFPKM = "CuffdiffSEDENTARY__transcript_FPKM_tracking.tabular",
+ isoformDiff = "CuffdiffSEDENTARY__transcript_differential_expression_testing.tabular",
+ TSSFPKM = "CuffdiffSEDENTARY__TSS_groups_FPKM_tracking.tabular",
+ TSSDiff = "CuffdiffSEDENTARY__TSS_groups_differential_expression_testing.tabular",
+ CDSFPKM = "CuffdiffSEDENTARY__CDS_FPKM_tracking.tabular",
+ CDSExpDiff = "CuffdiffSEDENTARY__CDS_FPKM_differential_expression_testing.tabular"",
+ CDSDiff = "CuffdiffSEDENTARY__CDS_overloading_diffential_expression_testing.tabular",
+ promoterFile = "CuffdiffSEDENTARY__promoters_differential_expression_testing.tabular",
+ splicingFile = "CuffdiffSEDENTARY__splicing_differential_expression_testing.tabular",
+ rebuild = T)
I think I'm missing something really obvious here!
Thank you so much!
Kelesy
Sorry to bother with a simple question- I have read through all the cummeRbund posts and tutorials but I seem to be stuck right at the start!
I have ran RNA-seq analyses on galaxy online- tophat, cufflinks, cuffmerge, and cuffdiff. I would now like to visualize results in cummeRbund. I downloaded the cuffdiff files (11 each for two groups) off galaxy and they are in .tabular format. I installed cummeRbund, and ran the following. It does not work. Could the issue be that files should be in .db format? I don't know where the cuffData.db file came from- it appeared before I had even downloaded the cuffdiff files.
> source("http://bioconductor.org/biocLite.R")
> biocLite("cummeRbund")
> getwd()
> setwd("C:/Users/caetano1/Downloads/SEDENTARYDFF")
> list.files()
> library(cummeRbund)
> cuff= readCufflinks (dbFile = "cuffData.db",
+ geneFPKM = "CuffdiffSEDENTARY__gene_FPKM_tracking.tabular",
+ geneDiff = "CuffdiffSEDENTARY__CDS_FPKM_differential_expression_testing.tabular",
+ isoformFPKM = "CuffdiffSEDENTARY__transcript_FPKM_tracking.tabular",
+ isoformDiff = "CuffdiffSEDENTARY__transcript_differential_expression_testing.tabular",
+ TSSFPKM = "CuffdiffSEDENTARY__TSS_groups_FPKM_tracking.tabular",
+ TSSDiff = "CuffdiffSEDENTARY__TSS_groups_differential_expression_testing.tabular",
+ CDSFPKM = "CuffdiffSEDENTARY__CDS_FPKM_tracking.tabular",
+ CDSExpDiff = "CuffdiffSEDENTARY__CDS_FPKM_differential_expression_testing.tabular"",
+ CDSDiff = "CuffdiffSEDENTARY__CDS_overloading_diffential_expression_testing.tabular",
+ promoterFile = "CuffdiffSEDENTARY__promoters_differential_expression_testing.tabular",
+ splicingFile = "CuffdiffSEDENTARY__splicing_differential_expression_testing.tabular",
+ rebuild = T)
I think I'm missing something really obvious here!
Thank you so much!
Kelesy
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